Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium.

BACKGROUND: WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES: Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS: Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION: In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS: Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.

Increase of Severe Pulmonary Infections in Adults Caused by M1UK Streptococcus pyogenes, Central Scotland, UK.

We characterized the epidemiology, host-pathogen characteristics, and outcomes of severe adult pulmonary Streptococcus pyogenes infections that coincided with a high community caseload in central Scotland, UK. The pulmonary infections had high illness and death rates and were associated with socioeconomic deprivation, influenza A co-infection, and the M1UK lineage of S. pyogenes.

Candida auris: a Review of the Literature.

The emerging pathogen Candida auris has been associated with nosocomial outbreaks on five continents. Genetic analysis indicates the simultaneous emergence of separate clades of this organism in different geographical locations. Invasive infection and colonization have been detected predominantly in patients in high-dependency settings and have garnered attention due to variable antifungal resistance profiles and transmission within units instituting a range of infection prevention and control measures. Issues with the identification of C. auris using both phenotypic and molecular techniques have raised concerns about detecting the true scale of the problem. This review considers the literature available on C. auris and highlights the key unknowns, which will provide direction for further work in this field.

Correction to: Fidaxomicin for the treatment of Clostridium difficile infection (CDI) in at-risk patients with inflammatory bowel disease, fulminant CDI, renal impairment or hepatic impairment: a retrospective study of routine clinical use (ANEMONE).

The article "Fidaxomicin for the treatment of Clostridium difficile infection (CDI) in at-risk patients with inflammatory bowel disease, fulminant CDI, renal impairment or hepatic impairment: a retrospective study of routine clinical use (ANEMONE)", written by M.J.G.T. Vehreschild et al., was originally published at Springerlink on 11 August 2018 without open access.

Fidaxomicin for the treatment of Clostridium difficile infection (CDI) in at-risk patients with inflammatory bowel disease, fulminant CDI, renal impairment or hepatic impairment: a retrospective study of routine clinical use (ANEMONE).

Information is limited or lacking on fidaxomicin treatment of Clostridium difficile infection (CDI) in patients with inflammatory bowel disease, fulminant or life-threatening CDI, severe renal impairment, moderate-to-severe hepatic impairment and pregnancy. The ANEMONE study investigated fidaxomicin use in a routine clinical setting, focusing on these medical conditions of specific interest (MCSIs). This retrospective, post-authorisation study reviewed hospital records from Austria, Germany, Spain and the UK (June 2012-June 2015), collecting data from hospital admission to 30 days after last fidaxomicin dose. The primary objective was to identify the proportion of fidaxomicin-treated patients with MCSIs. Secondary objectives were to describe 30-day mortality, changes in ECG and laboratory parameters, fidaxomicin exposure and CDI response (resolution of diarrhoea; 30-day recurrence). 45.3% (261/576) of patients had ≥ 1 MCSI. Thirty-day mortality (post-first dose) was 17.0% (98/576) in the total population and slightly higher (24.6-27.6%) in patients with fulminant CDI or severe renal impairment. 29.6% (24/81) deaths of known cause were attributable to CDI. Of changes in laboratory parameters or ECG findings, only a decrease in leucocyte counts appeared associated with fidaxomicin, consistent with a positive treatment response. Diarrhoea resolved in 78.0% (404/518) of treatment episodes; diarrhoea resolution was lowest in patients with fulminant CDI (investigator-defined, 67.5%, 56/88) and severe renal impairment (68.0%, 68/100). Thirty-day recurrence (18.8%, 79/420) was similar across MCSI subgroups. Although almost half of fidaxomicin-treated patients had ≥ 1 MCSI, the majority of patients in all subgroups had positive responses to treatment, and no particular safety concerns were identified.

The laboratory investigation, management, and infection prevention and control of Candida auris: a narrative review to inform the 2024 national guidance update in England.

The emergent fungal pathogen Candida auris is increasingly recognised as an important cause of healthcare-associated infections globally. It is highly transmissible, adaptable, and persistent, resulting in an organism with significant outbreak potential that risks devastating consequences. Progress in the ability to identify C. auris in clinical specimens is encouraging, but laboratory diagnostic capacity and surveillance systems are lacking in many countries. Intrinsic resistance to commonly used antifungals, combined with the ability to rapidly acquire resistance to therapy, substantially restricts treatment options and novel agents are desperately needed. Despite this, outbreaks can be interrupted, and mortality avoided or minimised, through the application of rigorous infection prevention and control measures with an increasing evidence base. This review provides an update on epidemiology, the impact of the COVID-19 pandemic, risk factors, identification and typing, resistance profiles, treatment, detection of colonisation, and infection prevention and control measures for C. auris. This review has informed a planned 2024 update to the United Kingdom Health Security Agency (UKHSA) guidance on the laboratory investigation, management, and infection prevention and control of Candida auris. A multidisciplinary response is needed to control C. auris transmission in a healthcare setting and should emphasise outbreak preparedness and response, rapid contact tracing and isolation or cohorting of patients and staff, strict hand hygiene and other infection prevention and control measures, dedicated or single-use equipment, appropriate disinfection, and effective communication concerning patient transfers and discharge.

Outcomes after Emergency Admission with a Diabetic Foot Attack Indicate a High Rate of Healing and Limb Salvage But Increased Mortality: 18-Month Follow-up Study.

AIM: The diabetic foot attack (DFA) is perhaps the most devastating form of diabetic foot infection, presenting with rapidly progressive skin and tissue necrosis, threatening both limb and life. However, clinical outcome data in this specific group of patients are not available. METHODS: Analysis of 106 consecutive patients who underwent emergency hospitalisation for DFA (TEXAS Grade 3B or 3D and Infectious Diseases Society of America (IDSA) Class 4 criteria). Outcomes evaluated were: 1) Healing 2) major amputation 3) death 4) not healed. The first outcome reached in one of these four categories over the follow-up period (18.4±3.6 months) was considered. We also estimated amputation free survival. RESULTS: Overall, 57.5% (n=61) healed, 5.6% (n=6) underwent major amputation, 23.5% (n=25) died without healing and 13.2% (n=14) were alive without healing. Predictive factors associated with outcomes were: Healing (age<60, p=0.0017; no Peripheral arterial disease (PAD) p= 0.002; not on dialysis p=0.006); major amputation (CRP>100 mg/L, p=0.001; gram+ve organisms, p=0.0013; dialysis, p= 0.001), and for death (age>60, p= 0.0001; gram+ve organisms p=0.004; presence of PAD, p=0.0032; CRP, p=0.034). The major amputation free survival was 71% during the first 12 months from admission, however it had reduced to 55.4% by the end of the follow-up period. CONCLUSIONS: In a unique population of hospitalised individuals with DFA, we report excellent healing and limb salvage rates using a dedicated protocol in a multidisciplinary setting. An additional novel finding was the concerning observation that such an admission was associated with high 18-month mortality, almost all of which was after discharge from hospital.

Admission Time Deep Swab Specimens Compared With Surgical Bone Sampling in Hospitalized Individuals With Diabetic Foot Osteomyelitis and Soft Tissue Infection.

Whether deep swab cultures taken at admission reliably identify pathogens compared to surgical bone specimens in hospitalized individuals with diabetic foot osteomyelitis and soft tissue infection is unclear. Comparison of microbiological isolates between a deep wound swab (DWS) taken at the time of admission through the actively infected, discharging ulcer probing to the bone and the subsequent surgical bone sample (SBS) taken during surgical debridement was made. A total of 63 subjects (age 60.8 ± 13.5 years, 75% male, 80% Type 2 diabetes, HbA1C 8.9%±2.2%) were included. The proportion of Gram-positive (DWS 49% v SBS 52%) and Gram-negative (DWS 60% v SBS 60%) isolates was similar between the techniques. However, the overall concordance of isolates between the two techniques was only fair (κ=0.302). The best concordance was observed for Staphylococcus aureus (κ=0.571) and MRSA (κ=0.644). There was a correlation between number of isolates in SBS with prior antibiotic therapy of any duration (r= -0.358, p=0.005) and with the duration of ulceration (r=0.296, p=0.045); no clinical correlations were found for DWS. Prior antibiotic therapy (p=0.03) and duration of ulceration <8 weeks (p=0.025) were predictive of negative growth on SBS. In conclusion, we found only a fair concordance between deep wound swabs acquired at admission and surgical bone specimens in those presenting with a severe diabetic foot infection and features of osteomyelitis. Ensuring early surgical debridement of all infected tissue and obtaining bone specimens should be considered a clinical priority, which may also reduce the likelihood of negative growth on SBS.

IncN3 and IncHI2 plasmids with an In1763 integron carrying bla IMP-1 in carbapenem-resistant Enterobacterales clinical isolates from the UK.

Introduction. Imipenemase (IMP) carbapenemase genes are relatively rare among Enterobacterales in the UK. Emergence in multiple hospitals, in different strains and species, prompted an investigation into their genetic context.Aim. Our goal was to identify and describe the elements carrying bla IMP genes in a variety of Enterobacterales from five hospitals in the UK.Methodology. Long-read nanopore sequencing was carried out on 18 IMP-positive isolates belonging to 6 species. The locations of the bla IMP genes and other associated genetic elements were identified.Results. Ten out of 18 isolates carried bla IMP-1 on an IncN3 plasmid (52-57 kb) in an In1763 class 1 integron. These plasmids also contained genes encoding type IV secretion and conjugal transfer proteins. Five out of 18 isolates carried bla IMP-1 in the same In1763 integron in much larger IncHI2 plasmids. A further isolate carried the In1763 integron in a chromosomally located plasmid fragment. Two isolates carried bla IMP-4 in IncHI2 plasmids. The isolates included three representatives of sequence type 20 of Klebsiella pneumoniae, with one carrying a distinct plasmid from the other two.Conclusion. Highly similar IncN3 plasmids were found in a range of Enterobacterales, mostly K. pneumoniae and the Enterobacter cloacae complex, from three of four London hospitals, with the same In1763 integron carrying bla IMP-1 also being found in IncHI2 plasmids and chromosomally. These plasmids carried multiple elements facilitating self-transmission. Strain typing alone was not sufficient to investigate cross-infection among this set of isolates, many of which appeared to be unrelated until plasmid analysis was undertaken, and vice versa.

Candida auris outbreak: Mortality, interventions and cost of sustaining control.

OBJECTIVE: Candida auris has recently emerged as a global cause of multidrug resistant fungal outbreaks. An outbreak occurred at a tertiary care center in London in 2016. Transmission characteristics, interventions, patient outcomes and cost of resources are described. METHODS: Outbreak interventions included patient isolation, contact screening, single-use equipment, environmental screening and decontamination, staff education, and enhanced surveillance. Risk factors for infection were recorded. Survival probabilities of patients with C. auris and other Candida bloodstream infections (BSI) were calculated. Antifungal susceptibility and epidemiological typing were performed. Actual and opportunity costs of interventions were determined. RESULTS: 34 patients acquired the organism including 8 with BSI. Clinical infection was significantly associated with prolonged hospital stay, haemodialysis and antifungal therapy. Variable susceptibility to amphotericin and the triazoles was seen and isolates clustered with the South Asian strains. No significant difference was detected in the survival probabilities of C. auris BSI compared to other candidemias. Outbreak control cost in excess of £1 million and £58,000/month during the subsequent year. CONCLUSION: C. auris outbreaks can be controlled by a concerted infection control strategy but can be expensive. Transmission maybe prolonged due to patient movements and unidentified transmission mechanisms.

A prospective study of community-associated Clostridium difficile infections: the role of antibiotics and co-infections.

OBJECTIVES: This prospective study was performed to determine the incidence, risk factors, severity and outcomes of community-associated Clostridium difficile infection (CA-CDI) in the SE of Scotland. METHODS: All patients (335) diagnosed with laboratory confirmed CDI in the city of Edinburgh, East Lothian and Midlothian regions of Scotland between August 2010 and July 2011 were followed up for one year after diagnosis. Clinical details and laboratory markers were recorded. Stool samples were tested for C. difficile, other bacterial pathogens and norovirus. Molecular epidemiology of C. difficile isolates was studied by PCR-ribotyping. RESULTS: Of the total 335 confirmed CDI cases, PCR-ribotype 001 was the commonest (14.1%), followed by PCR-ribotypes 078 (12.9%) and 015 (11.7%), respectively. CA-CDI represented 12.5% of the cases. In these, PCR-ribotype 078 was the commonest (19.0%), followed by PCR-ribotypes 014/020 (16.7%), PCR-ribotype 015 (14.3% and PCR-ribotype 001 (11.9%). A lower Charlson co-morbidity index and a lower age was observed in the CA-CDI group as was total number of different antibiotic classes whereas age >75 was more common in the HA-CDI group. On multivariable analysis presence of PCR-ribotype 078 was significantly associated with community acquisition (p = 0.006) whereas a greater proportion of immunosuppressed patients and those on antibiotics 8 weeks preceding diagnosis (p = 0.035 and p = 0.005 respectively) were found among HA-CDI cases. Charlson co-morbidity index, number of different antibiotics given in the eight weeks preceding onset, severity of infection and rural residence were not significantly different between the two groups. CONCLUSION: This study demonstrates that patients with CA-CDI may also present with severe infection, are less likely to receive antibiotics prior to CDI, more likely to be younger in age and have a greater proportion of PCR-ribotype 078 compared with CDI acquired in a hospital setting. Hence a high level of vigilance must be maintained to detect CDI cases which present in the community without the traditional predisposing factors.

Clostridium difficile infections in South East Scotland: mortality and recurrence in a region without PCR ribotype 027.

Three hundred and thirty-five patients with laboratory-confirmed Clostridium difficile infections (CDIs) were studied for epidemiological features, clinical presentation and laboratory markers. They were followed up for 1 year to determine recurrence and mortality. Four hundred and thirty-two episodes were recorded. One year mortality was 41.8 % of which CDI was listed on 20 % of the death certificates. One year recurrence rate was 22.9 %. PCR ribotype 001 was the commonest epidemiological type and ribotype 027 was not detected. High total leucocyte count and low albumin were significantly associated with mortality, as was the absence of a GI-invasive procedure in the 12 weeks preceding CDI diagnosis, probably due to patients being unfit for the procedure. No association with acid suppressants, deletion in the tdcC anti-sigma factor or vancomycin-resistant enterococcus/methicillin-resistant Staphylococcus aureus co-infection was detected. One year mortality was higher in patients who developed recurrent infections (P<0.001). Differences in ribotype were observed in 2.3 %, 11.11 %, 20 % and 32.4 % isolates with time intervals between sampling of 0-20, 21-40, 41-60 and >60 days, respectively, suggesting that the arbitrary cut-off of 28 days to call a repeat infection a reinfection may not be correct in some cases.

Changes in antibiotic susceptibility and ribotypes in Clostridium difficile isolates from southern Scotland, 1979-2004.

An increase in the incidence of clinical cases of Clostridium difficile infection has been reported in recent years, but few studies have examined changes in molecular epidemiology and antibiotic resistance over a long period of time. A collection of 179 isolates of C. difficile obtained from symptomatic adult patients in southern Scotland between 1979 and 2004 was used to determine changes in the prevalence of epidemiological types and antibiotic susceptibilities to common antibiotics. PCR ribotyping and MIC determination were performed on all isolates. A total of 56 different ribotypes were identified, among which ribotype 002 was the commonest type overall (14 .0%), followed by ribotypes 014 (7.3 %), 012 (5 .0%), 015 (5.0 %), 020 (5 .0%) and 001 (4.5 %). Ribotype 078 was also identified. The 10 commonest ribotypes comprised 55 % of the total isolates. Ribotype 001 increased in prevalence from 1.5 to 12.2 % over the study years, whereas the prevalence of ribotype 012 decreased from 8.7 to 2 .0%. Resistance to clindamycin, erythromycin and ceftriaxone was found in 95.5, 14.0 and 13.4 % of isolates, respectively. Resistance to vancomycin or metronidazole was not detected. Thirty-two (17.9 %) and 14 (7.8 %) isolates were resistant to two and three or more antibiotics, respectively. Ribotype 001 displayed maximum resistance, with 50 % of isolates resistant to erythromycin, moxifloxacin and ceftriaxone, and 100 % resistant to clindamycin. Over the 26 years of the study, antibiotic resistance and ribotype prevalence have changed, and antibiotic pressures may have been the major driver of this change.